RetrogeneDB ID: retro_dord_220

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_5906:709764..710116(+)
• Located in intron of: ENSDORG00000015920

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Supt4a
• Ensembl ID: ENSDORG00000002826
• Aliases: None
• Description: suppressor of Ty 4A [Source:MGI Symbol;Acc:MGI:107416]

Sequence

>retro_dord_220
ATGGCCCTGGAGACAGTCTGAAGGATCTGTGGCATCTGTGGGCGGGTCCGCTGTATTCACTGGTCAAGACTATAGACCAG
ATTGAATATGATGGATATGATCATTGTGATGCATTTCTACAAGTGAAGGGTAACAGAGAAATGGTAGATGACTGCACCAG
CTCTTCCTTTGATGGGAATCATTGCAATGATGAGTCCAGAGGACAACTGGCTCTCCAAGTGGCAGCGAGTCAGTAACTTT
AAGTCAGGTGTATATGTTGTGGCAGTCACTGGTTGCCTGCCCCCAAGGAATTATACAGGAGCTAAAAAGTCGAGGAGTGG
CCTACAAATCCATAGTCACTGTTACAAAAACC

Alignment

ORF - retro_dord_220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALETV-PKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDG-IIAMMSPED
          MALETV..KDL.HL.A..L.SLVKTIDQ.EYDG.D.CDA.LQ.KGNREMV.DCTSSSFDG.IIAMMSPED
Retrocopy MALETV<LKDLWHLWAGPLYSLVKTIDQIEYDGYDHCDAFLQVKGNREMVDDCTSSSFDG>IIAMMSPED

Parental  SWVSKWQRVSNFKPGVYAVSVTGRL-PQGIVRELKSRGVAYKSRDTAIKT
          .W.SKWQRVSNFK.GVY.V.VTG.L.PQGI..ELKSRGVAYKS..T..KT
Retrocopy NWLSKWQRVSNFKSGVYVVAVTGCL>PQGIIQELKSRGVAYKSIVTVTKT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_220 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017369	3 retrocopies	retro_cjac_1196, retro_cjac_1990, retro_cjac_4216,
Dipodomys ordii	ENSDORG00000002826	2 retrocopies	retro_dord_177, retro_dord_220 ,
Macropus eugenii	ENSMEUG00000010164	1 retrocopy	retro_meug_2079,
Myotis lucifugus	ENSMLUG00000025583	1 retrocopy	retro_mluc_761,
Otolemur garnettii	ENSOGAG00000031972	1 retrocopy	retro_ogar_2702,